Is there any way to save different Startup Files?
Not currently natively supported, but it is planned for future 2.8 versions.

However nothing stops you from having several template files saved somewhere safe in your computer, and opening them as startup templates.

Create a "Startup Files Library" somewhere in your hard drive, and save all your desired startup files there.

You can add the folder as favorite to Blender's built in file manager, and readily open any file from there whenever you require a specific task.

If you open them frequently they may even get listed in the splash screen at startup for easier access.

One other neat trick you may use is to manually lock your recent-files.txtas read only, and manually edit it to include only your desired startup files, if you don't mind loosing the convenience of having other recently opened projects readily accessible that is.

It is just a simple plain-text file with one file path per line, so you can edit it externally with any notepad like or programmer's plain-text editor editor.

If you know how to code you can also use the Python API or create an addon for your convenience.

You may also create several desktop shortcuts (or Start Menu or saved them anywhere else you like) each with a different command line parameter, specifying a passed file for Blender to open, effectively starting it as a template. All you have to do then is Save-As to the desired location.